Announcing the Program namd
William F. Humphrey
billh at lisboa.ks.uiuc.edu
Mon Jul 3 16:13:14 EST 1995
Announcing the Program namd
The Theoretical Biophysics group at the University of Illinois and the
Beckman Institute would like to announce the availability the program namd,
a new package for high performance parallel molecular dynamics simulations.
This software is being made available to the structural biology research
community free of charge, and includes the source code for namd, documentation,
and precompiled binaries for various parallel platforms The documentation,
in postscript form, includes a programmers guide and a users guide.
A more complete description of namd is available via the namd WWW home page:
The software itself is available via anonymous ftp in the directory:
namd is a molecular dynamics program designed to provide high performance
simulations for large biological molecular systems. Specifically, namd
achieves high performance by exploiting the power of parallel computers
and by providing a modular design that facilitates the implementation
of new algorithms. A high degree of modularity is obtained by using an
object-oriented design and implementation in C++. namd uses spatial
decomposition coupled with a multithreaded, message-driven design, which
provides a scalable, efficient parallel framework. namd also incorporates
the Distributed Parallel Multipole Tree Algorithm (DPMTA) developed by the
Scientific Computing group at Duke University, which allows full electrostatic
force evaluation in O(N) time. As part of the MDScope system, namd
is connected via the communication system MDComm to the molecular graphics
program VMD (also developed by the Theoretical Biophysics group) to provide
such an interactive system where researchers can view and interact with a
The program has many features, which include:
o Input and output file compatibility with X-PLOR
o CHARMM19 and CHARMM22 parameter support
o Support for traditional MD functions such as energy minimization,
velocity rescaling, harmonic boundary conditions, harmonic
atom restraints, etc.
o Full electrostatic evaluation using DPMTA from Duke University
integrated using a multiple timestep integration scheme. For
more information on DPMTA, see the Scientific Computing home
o Spatial decomposition for O(N/P) scalability of memory, computation,
o Message-driven, multithread design for high performance parallel
o Modular, extensible source code using an object-oriented design in
C++, with a programmers guide describing the source code structure.
o Portable parallelism provided by PVM and Charm++ communication
o Integration with the program VMD, a molecular graphics
program developed in the Theoretical Biophysics Group
at the University of Illinois.
See the VMD WWW home page for more info:
VMD can be used to set up and concurrently display a MD simulation
using NAMD. The two programs, along with the intermediary
communications package (called MDComm) constitute the 'MDScope'
namd should run on any parallel platform with a C++ compiler and PVM
version 3.3.6 or later. Tested Makefiles are included for clusters
of HP, SGI, and IBM workstations, Cray T3D, and Convex Exemplar.
Precompiled binaries are provided for HP and SGI workstations.
VMD, NAMD, and the entire MDScope environment are part of an ongoing project
within the Theoretical Biophysics group to help provide free, effective tools
for molecular dynamics studies in structural biology. This project is funded
by the National Institutes of Health and the National Science Foundation.
/* Bill Humphrey (billh at ks.uiuc.edu) */
/* Theoretical Biophysics | Nothing matters but */
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